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1.  A Comprehensive Analysis of the Transcriptomes of Marssonina brunnea and Infected Poplar Leaves to Capture Vital Events in Host-Pathogen Interactions 
PLoS ONE  2015;10(7):e0134246.
Background
Understanding host-pathogen interaction mechanisms helps to elucidate the entire infection process and focus on important events, and it is a promising approach for improvement of disease control and selection of treatment strategy. Time-course host-pathogen transcriptome analyses and network inference have been applied to unravel the direct or indirect relationships of gene expression alterations. However, time series analyses can suffer from absent time points due to technical problems such as RNA degradation, which limits the application of algorithms that require strict sequential sampling. Here, we introduce an efficient method using independence test to infer an independent network that is exclusively concerned with the frequency of gene expression changes.
Results
Highly resistant NL895 poplar leaves and weakly resistant NL214 leaves were infected with highly active and weakly active Marssonina brunnea, respectively, and were harvested at different time points. The independent network inference illustrated the top 1,000 vital fungus-poplar relationships, which contained 768 fungal genes and 54 poplar genes. These genes could be classified into three categories: a fungal gene surrounded by many poplar genes; a poplar gene connected to many fungal genes; and other genes (possessing low degrees of connectivity). Notably, the fungal gene M6_08342 (a metalloprotease) was connected to 10 poplar genes, particularly including two disease-resistance genes. These core genes, which are surrounded by other genes, may be of particular importance in complicated infection processes and worthy of further investigation.
Conclusions
We provide a clear framework of the interaction network and identify a number of candidate key effectors in this process, which might assist in functional tests, resistant clone selection, and disease control in the future.
doi:10.1371/journal.pone.0134246
PMCID: PMC4519268  PMID: 26222429
2.  Effective Inhibition of c-MET-mediated Signaling, Growth, and Migration of Ovarian Cancer Cells is Influenced by the Ovarian Tissue Microenvironment 
Oncogene  2013;34(2):144-153.
The signaling mediated by c-MET and its ligand, hepatocyte growth factor (HGF), has been implicated in malignant progression of cancer involving stimulation of proliferation, invasion, and metastasis. We studied the c-MET/HGF axis as a mediator of tumor-stromal interaction in ovarian cancer and the value of targeting c-MET for the treatment of ovarian cancer. To assess c-MET signaling, we established in vitro models of the microenvironment using primary and immortalized human fibroblasts from normal ovary and tumor samples and epithelial ovarian cancer cell lines. We found that fibroblast from normal ovaries secreted high levels of HGF (1,500 to 3,800 pg/mL) as compared to tumor-derived fibroblasts (undetectable level) and could elicit cellular biological responses on c-MET expressing ovarian cancer cells including increase of cell proliferation and migration (2- to 140-fold increase). HGF secreted by fibroblasts was also found sequestered within extracellular matrices (ECMs) and when degraded this ECM-derived HGF stimulated cancer cell migration (1.5- to 24-fold). In cells containing constitutive c-MET phosphorylation, recombinant HGF and fibroblast-derived HGF negligibly affect c-MET phosphorylation on Tyr1234 and Tyr1003. However, both sources of HGF increased the phosphorylation of c-MET on Tyr1349, the multi-substrate docking site, by more than 6-fold and led to activation of downstream signaling transducers. DCC-2701 (Deciphera Pharmaceuticals, LLC), a novel c-MET/TIE-2/VEGFR inhibitor was able to effectively reduce tumor burden in vivo and block c-MET pTyr1349-mediated signaling, cell growth, and migration as compared to a HGF antagonist in vitro. Importantly, DCC-2701’s anti-proliferative activity was dependent on c-MET activation induced by stromal human fibroblasts and to a lesser extent exogenous HGF. Our data suggest for the first time that DCC-2701 may be superior to HGF antagonists that are in clinical trials and that pTyr1349 levels might be a good indicator of c-MET activation and likely response to targeted therapy as a result of signals from the microenvironment.
doi:10.1038/onc.2013.539
PMCID: PMC4067476  PMID: 24362531
Ovarian cancer; Human ovarian fibroblast; c-MET; Hepatocyte growth factor; DCC-2701
3.  Clinical predictors of severe cerebral amyloid angiopathy and influence of APOE genotype in persons with pathologically-verified Alzheimer’s disease 
JAMA neurology  2014;71(7):878-883.
Importance
Though cerebral amyloid angiopathy (CAA) has important clinical implications, our understanding of it and ability to diagnose it is limited.
Objective
We sought to determine pathological correlates and clinical factors identifiable during life that predict the presence of severe CAA in persons with pathologically-confirmed Alzheimer’s disease (AD).
Design
We compared demographic and clinical variables at the earliest visit during life at which subjects were found to have cognitive impairment, and pathological variables between persons ultimately found to have no or severe CAA at autopsy using logistic regression. Analyses were repeated separately for carriers and non-carriers of the APOE ε4 allele.
Setting
Data were obtained from the Uniform Data Set that comprises longitudinal clinical assessments performed in the Alzheimer’s Disease Centers funded by the National Institute on Aging.
Participants
193 persons with severe CAA and 232 persons with no CAA. All subjects had cognitive impairment and met NIA-Reagan neuropathological criteria for AD.
Main Outcome Measures
Prevalence of demographic characteristics and the APOE ε4 allele and odds ratios of clinical variables for the prediction of severe CAA.
Results
Persons with severe CAA were more likely to carry an APOE ε4 allele (64.9% vs. 42.8%), to be Hispanic (6.8% vs. 1.3%, p = 0.003), to have had a transient ischemic attack (TIA, 12.5% vs. 6.1%, OR = 2.1, 95% CI = 1 – 4.4), and had lower degrees of diffuse amyloid plaque pathology (mean CERAD scores 1.2 vs. 1.4, p = 0.01) than persons with no CAA. Intracerebral hemorrhage (9.3% vs. 3.5%, p = 0.01), cortical microinfarcts (20.7% vs. 12.9%, p = 0.03), and subcortical leukoencephalopathy (20.5% vs. 12.1%, p = 0.02) were more common in persons with CAA. A higher prevalence of stroke (11.1% vs. 3.9%, OR = 3.8, 95% CI 1.0 – 14.6) and hypercholesterolemia (50% vs. 33.3%, OR = 2.3, CI 1.1 – 4.7) were found in non-carriers of the ε4 allele with severe CAA.
Conclusions and Relevance
Being Hispanic and having had a TIA-like episode were predictors of CAA in persons with AD. Less diffuse parenchymal amyloid pathology in persons with severe CAA suggests a difference in Aβ trafficking.
doi:10.1001/jamaneurol.2014.681
PMCID: PMC4101018  PMID: 24797962
4.  An interferon-beta promoter reporter assay for high throughput identification of compounds against multiple RNA viruses 
Antiviral research  2014;107:56-65.
Virus infection of host cells is sensed by innate pattern recognition receptors (PRRs) and induces production of type I interferons (IFNs) and other inflammatory cytokines. These cytokines orchestrate the elimination of the viruses but are occasionally detrimental to the hosts. The outcomes and pathogenesis of viral infection are largely determined by the specific interaction between the viruses and their host cells. Therefore, compounds that either inhibit viral infection or modulate virus-induced cytokine response should be considered as candidates for managing virus infection. The aim of the study was to identify compounds in both categories, using a single cell-based assay. Our screening platform is a HEK293 cell-based reporter assay where the expression of a firefly luciferase is under the control of a human IFN-β promoter. We have demonstrated that infection of the reporter cell line with a panel of RNA viruses activated the reporter gene expression that correlates quantitatively with the levels of virus replication and progeny virus production, and could be inhibited in a dose-dependent manner by known antiviral compound or inhibitors of PRR signal transduction pathways. Using Dengue virus as an example, a pilot screening of a small molecule library consisting of 26,900 compounds proved the concept that the IFN-β promoter reporter assay can serve as a convenient high throughput screening platform for simultaneous discovery of antiviral and innate immune response modulating compounds. A representative antiviral compound from the pilot screening, 1-(6-ethoxybenzo[d]thiazol-2-yl)-3-(3-methoxyphenyl) urea, was demonstrated to specifically inhibit several viruses belonging to the family of flaviviridae.
doi:10.1016/j.antiviral.2014.04.010
PMCID: PMC4143146  PMID: 24792753
high throughput assay; antiviral; innate immune modulator; dengue virus
5.  Lycopene Attenuates Colistin-Induced Nephrotoxicity in Mice via Activation of the Nrf2/HO-1 Pathway 
Nephrotoxicity is the major dose-limiting factor for the clinical use of colistin against multidrug-resistant (MDR) Gram-negative bacteria. This study aimed to investigate the protective effect of lycopene on colistin-induced nephrotoxicity in a mouse model. Fifty mice were randomly divided into 5 groups: the control group (saline solution), the lycopene group (20 mg/kg of body weight/day administered orally), the colistin group (15 mg/kg/day administered intravenously), the colistin (15 mg/kg/day) plus lycopene (5 mg/kg/day) group, and the colistin (15 mg/kg/day) plus lycopene (20 mg/kg/day) group; all mice were treated for 7 days. At 12 h after the last dose, blood was collected for measurements of blood urea nitrogen (BUN) and serum creatinine levels. The kidney tissue samples were obtained for examination of biomarkers of oxidative stress and apoptosis, histopathological assessment, and quantitative reverse transcription-PCR (qRT-PCR) analysis. Colistin treatment significantly increased concentrations of BUN and serum creatinine, tubular apoptosis/necrosis, lipid peroxidation, and heme oxygenase 1 (HO-1) activity, while the treatment decreased the levels of endogenous antioxidant biomarkers glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD). Notably, the changes in the levels of all biomarkers were attenuated in the kidneys of mice treated with colistin by lycopene (5 or 20 mg/kg). Lycopene treatment, especially in the colistin plus lycopene (20 mg/kg) group, significantly downregulated the expression of NF-κB mRNA (P < 0.01) but upregulated the expression of nuclear factor erythroid 2-related factor 2 (Nrf2) and HO-1 mRNA (both P < 0.01) in the kidney compared with the results seen with the colistin group. Our data demonstrated that coadministration of 20 mg/kg/day lycopene can protect against colistin-induced nephrotoxicity in mice. This effect may be attributed to the antioxidative property of lycopene and its ability to activate the Nrf2/HO-1 pathway.
doi:10.1128/AAC.03925-14
PMCID: PMC4291401  PMID: 25385104
6.  Occurrence and Characterization of Cronobacter spp. in Dehydrated Rice Powder from Chinese Supermarket 
PLoS ONE  2015;10(7):e0131053.
Cronobacter spp. are emerging food-borne pathogens and have been identified as causative agents of meningitis and necrotizing enterocolitis in infants. Dehydrated rice is popular with a wide range of people and it is frequently used as a substitute for infant milk powder to baby older than four months. The occurrence of Cronobacter spp. was investigated in 1,012 samples of dehydrated rice powder collected from 14 manufacturers in China during 2010 to 2012. The isolates were identified using fusA allele sequencing and subtyped using pulsed-field gel electrophoresis. Seventy-six samples (7.5%) contained Cronobacter spp. The prevalence among manufacturers ranged from 0-28.8%. The 76 isolates included 4 species [Cronobacter sakazakii (52 isolates) Cronobacter malonaticus (14 isolates), Cronobacter dublinensis (7 isolates), and Cronobacter muytjensii (3 isolates)]. Twenty-three unique fusA alleles and sixty-six PFGE-patterns were detected. All isolated strains were observed to be sensitive or to show intermediate susceptibility to eight tested antimicrobial agents. The study revealed serious contamination of dehydrated rice powder by Cronobacter spp., with prevalence varying among manufacturers in China. Identified Cronobacter species, fusA alleles, and subtypes were diverse.
doi:10.1371/journal.pone.0131053
PMCID: PMC4488472  PMID: 26132635
7.  Rhein: A Review of Pharmacological Activities 
Rhein (4, 5-dihydroxyanthraquinone-2-carboxylic acid) is a lipophilic anthraquinone extensively found in medicinal herbs, such as Rheum palmatum L., Cassia tora L., Polygonum multiflorum Thunb., and Aloe barbadensis Miller, which have been used medicinally in China for more than 1,000 years. Its biological activities related to human health are being explored actively. Emerging evidence suggests that rhein has many pharmacological effects, including hepatoprotective, nephroprotective, anti-inflammatory, antioxidant, anticancer, and antimicrobial activities. The present review provides a comprehensive summary and analysis of the pharmacological properties of rhein, supporting the potential uses of rhein as a medicinal agent.
doi:10.1155/2015/578107
PMCID: PMC4491579  PMID: 26185519
8.  Magnetic skyrmion transistor: skyrmion motion in a voltage-gated nanotrack 
Scientific Reports  2015;5:11369.
Magnetic skyrmions are localized and topologically protected spin configurations, which are of both fundamental and applied interests for future electronics. In this work, we propose a voltage-gated skyrmion transistor within the well-established framework of micromagnetics. Its operating conditions and processes have been theoretically investigated and demonstrated, in which the gate voltage can be used to switch on/off a circuit. Our results provide the first time guidelines for practical realization of hybrid skyrmionic-electronic devices.
doi:10.1038/srep11369
PMCID: PMC4471904  PMID: 26087287
9.  Simultaneous Removal of Lindane, Lead and Cadmium from Soils by Rhamnolipids Combined with Citric Acid 
PLoS ONE  2015;10(6):e0129978.
This study investigated the performance of rhamnolipids-citric acid mixed agents in simultaneous desorption of lindane and heavy metals from soils. The capacity of the mixed agents to solubilize lindane, lead and cadmium in aqueous solution was also explored. The results showed that the presence of citric acid greatly enhanced the solubilization of lindane and cadmium by rhamnolipids. A combined effect of the mixed agents on lindane and heavy metals removal from soils was observed. The maximum desorption ratios for lindane, cadmium and lead were 85.4%, 76.4% and 28.1%, respectively, for the mixed agents containing 1% rhamnolipidsand 0.1 mol/L citric acid. The results also suggest that the removal efficiencies of lead and cadmium were strongly related to their speciations in soils, and metals in the exchangeable and carbonate forms were easier to be removed. Our study suggests that the combining use of rhamnolipids and citric acid is a promising alternative to simultaneously remove organochlorine pesticides and heavy metals from soils.
doi:10.1371/journal.pone.0129978
PMCID: PMC4472516  PMID: 26087302
10.  Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals 
Journal of proteomics  2014;113:194-205.
Endometriosis, ectopic growth of the uterine lining (endometrium), which affects 6–11% of reproductive age women, is associated with pelvic pain and infertility. We investigated the peritoneal fluid (PF), urine and omental fat (OF) proteomes of women with endometriosis vs. individuals with no surgically visualized endometriosis. All participants were enrolled in the NICHD-funded ENDO Study. A two-step proteomic study was performed. The first, a broad survey, employed a semi-quantitative gel LC-mass spectrometry (MS) workflow: SDS PAGE fractionation, trypsin digestion and LC–MS/MS. The results showed sample integrity but failed to detect any differences between women with and without endometriosis. The second step was a quantitative analysis of OF samples. We employed another sample set (n = 30) from women ± disease and isobaric mass-tag (iTRAQ) chemistry to label peptides and 2D LC–MS/MS for protein identification and quantification. Three proteins—matrix metalloproteinase-9, neutrophil elastase, and FAM49B—were significantly lower in abundance in samples from women with endometriosis. Interestingly, neutrophil elastase and FAM49B levels were associated with higher levels of a subset of endocrine disrupting chemicals (EDCs) that were previously measured in the same samples. The results of these experiments showed the feasibility of associating endometriosis with changes in the OF protein repertoire and EDC levels.
Biological significance
Endometriosis, pathological growth of the uterine lining, is associated with significant morbidities, including pain and infertility. However, the causes of this common condition are poorly understood. This study determined whether endometriosis was associated with changes in the protein composition of peritoneal fluid, urine and/or omental fat. A protein of unknown function (FAM49B) and two proteinases (metalloproteinase-9, neutrophil elastase) were down regulated in OF samples from women with versus without endometriosis. These findings suggested proteinase imbalances at sites that were distant from the endometriotic lesions. Additionally, FAM49B and neutrophil elastase levels were associated with higher levels of a subset of environmental chemicals that were quantified in the same samples, suggesting other possible associations. Thus, this work generated hypotheses that will be tested in further studies.
doi:10.1016/j.jprot.2014.09.015
PMCID: PMC4467531  PMID: 25284053
Endometriosis; Peritoneal fluid; Urine; Omental fat; Mass spectrometry; Environmental chemicals
11.  Unplanned Quitting in a Triethnic Sample of U.S. Smokers 
Nicotine & Tobacco Research  2014;16(6):759-765.
Introduction:
Smokers who report quitting without prior planning have been shown to report longer abstinence compared with those who planned. Little is known about unplanned quitting (UQ) among U.S. smokers, minorities, or nondaily and light smokers.
Methods:
Using an online panel, we recruited equal numbers of Black, White, and Latino nondaily, light daily, and moderate/heavy daily smokers. Of the 1,127 who reported a past-year quit attempt, we queried whether it was planned and the maximum number of days abstinent.
Results:
Overall, 38% reported that their last quit attempt was unplanned. The impact of planned versus unplanned quitting interacted with smoking level and race. Among White moderate/heavy smokers, mean days abstinent was 99 for those who reported an unplanned quit attempt compared with 60 days for those who reported a planned attempt (p = .02). Among Black moderate/heavy smokers, the mean days abstinent was higher among those whose last attempt was planned, 92 days, compared with 56 days among those whose last attempt was unplanned (p = .09). The pattern among Latinos resembled Whites but was not significant. Results remained after adjusting for confounds such as age, gender, education, income, time to first cigarette, and menthol use. There were no significant differences in abstinence by quit type for light or nondaily smokers.
Conclusions:
Future studies are needed to elucidate why UQ appears to have differential effectiveness across racial/ethnic groups and different levels of cigarette use. Research examining the impact of UQ on long-term quitting, which is not addressed here, is needed.
doi:10.1093/ntr/ntt272
PMCID: PMC4064007  PMID: 24420329
12.  The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules 
The ISME Journal  2014;8(6):1186-1197.
Quorum sensing (QS) signalling has been extensively studied in single species populations. However, the ecological role of QS in complex, multi-species communities, particularly in the context of community assembly, has neither been experimentally explored nor theoretically addressed. Here, we performed a long-term bioreactor ecology study to address the links between QS, organization and composition of complex microbial communities. The conversion of floccular biomass to highly structured granules was found to be non-random, but strongly and positively correlated with N-acyl-homoserine-lactone (AHL)-mediated QS. Specific AHLs were elevated up to 100-fold and were strongly associated with the initiation of granulation. Similarly, the levels of particular AHLs decreased markedly during the granular disintegration phase. Metadata analysis indicated that granulation was accompanied by changes in extracellular polymeric substance (EPS) production and AHL add-back studies also resulted in increased EPS synthesis. In contrast to the commonly reported nanomolar to micromolar signal concentrations in pure culture laboratory systems, QS signalling in the granulation ecosystem occurred at picomolar to nanomolar concentrations of AHLs. Given that low concentrations of AHLs quantified in this study were sufficient to activate AHL bioreporters in situ in complex granular communities, AHL mediated QS may be a common feature in many natural and engineered ecosystems, where it coordinates community behaviour.
doi:10.1038/ismej.2013.240
PMCID: PMC4030234  PMID: 24430488
biofilm; granulation; model ecosystem; mixed microbial communities; population; quorum sensing
13.  Impact of Continuous Quality Improvement Initiatives on Clinical Outcomes in Peritoneal Dialysis 
♦ Objective: We evaluated the role of a quality improvement initiative in improving clinical outcomes in peritoneal dialysis (PD).
♦ Methods: In a retrospective analysis of 6 years of data from a hospital registry, the period between 1 July 2005 and 30 June 2008 (control group) provided baseline data from before implementation of systemic outcomes monitoring, and the period between 1 July 2008 and 30 June 2011 [continuous quality improvement (CQI) group] represented the time when a CQI program was in place. Peritonitis incidence, patient and technique survival, cardiovascular status, causes of death, and drop-out were compared between the groups.
♦ Results: In the 370 patients of the CQI group and the 249 patients of the control group, the predominant underlying kidney diseases were chronic glomerulonephritis and diabetic nephropathy. After implementation of the CQI initiative, the peritonitis rate declined to 1 episode in 77.25 patient-months from 1 episode in 22.86 patient-months. Ultrasound parameters of cardiac structure were generally unchanged in the CQI group, but significant increases in cardiothoracic ratio and interventricular septal thickness were observed in the control group (both p < 0.05). Patient survival at 1, 2, and 3 years was significantly higher in the CQI group (97.3%, 96.3%, and 96.3% respectively) than in the control group (92.6%, 82.4%, and 67.3% respectively, p < 0.001). Implementation of the CQI initiative also appeared to significantly improve technique survival rates: 95.6%, 92.6%, and 92.6% in the CQI group compared with 89.6%, 79.2%, and 76.8% in the control group (p < 0.001) after 1, 2, and 3 years respectively.
♦ Conclusion: Integration of a CQI process into a PD program can significantly improve the quality of therapy and its outcomes.
doi:10.3747/pdi.2013.00123
PMCID: PMC4076962  PMID: 24962962
Continuous quality improvement; outcomes
14.  Compounds identified by virtual docking to a tetrameric EGFR extracellular domain can modulate Grb2 internalization 
BMC Cancer  2015;15:436.
Background
Overexpression or mutation of the epidermal growth factor receptor (EGFR) potently enhances the growth of many solid tumors. Tumor cells frequently display resistance to mechanistically-distinct EGFR-directed therapeutic agents, making it valuable to develop therapeutics that work by additional mechanisms. Current EGFR-targeting therapeutics include antibodies targeting the extracellular domains, and small molecules inhibiting the intracellular kinase domain. Recent studies have identified a novel prone extracellular tetrameric EGFR configuration, which we identify as a potential target for drug discovery.
Methods
Our focus is on the prone EGFR tetramer, which contains a novel protein-protein interface involving extracellular domain III. This EGFR tetramer is computationally targeted for stabilization by small molecule ligand binding. This study performed virtual screening of a Life Chemicals, Inc. small molecule library of 345,232 drug-like compounds against a molecular dynamics simulation of protein-protein interfaces distinct to the novel tetramer. One hundred nine chemically diverse candidate molecules were selected and evaluated using a cell-based high-content imaging screen that directly assessed induced internalization of the EGFR effector protein Grb2. Positive hits were further evaluated for influence on phosphorylation of EGFR and its effector ERK1/2.
Results
Fourteen hit compounds affected internalization of Grb2, an adaptor responsive to EGFR activation. Most hits had limited effect on cell viability, and minimally influenced EGFR and ERK1/2 phosphorylation. Docked hit compound poses generally include Arg270 or neighboring residues, which are also involved in binding the effective therapeutic cetuximab, guiding further chemical optimization.
Conclusions
These data suggest that the EGFR tetrameric configuration offers a novel cancer drug target.
Electronic supplementary material
The online version of this article (doi:10.1186/s12885-015-1415-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12885-015-1415-6
PMCID: PMC4451962  PMID: 26016476
Epidermal growth factor receptor; Grb2; Protein multimerization; Extracellular domain
15.  C/EBPδ MAINTAINS AMELOGENIN EXPRESSION IN THE ABSENCE OF C/EBPα, IN VIVO 
The Journal of biological chemistry  2007;282(41):29882-29889.
C/EBPα is implicated to regulate mouse amelogenin gene expression during tooth enamel formation, in vitro. Since enamel formation occurs during postnatal development and C/EBPα-deficient mice die at birth, we used the Cre/loxP recombination system to characterize amelogenin expression in C/EBPα conditional knock-out mice. Mice carrying the Cre-transgene under the control of the human keratin-14 (K14) promoter show robust Cre expression in the ameloblast cell lineage. Mating between mice bearing the floxed C/EBPα allele with K14-Cre mice generate C/EBPα conditional knock-out mice. Real-time PCR analysis shows that removal of one C/EBPα allele from the molar enamel epithelial organ of 3-day postnatal mice results in dramatic decrease in endogenous C/EBPα mRNA levels and coordinately altered amelogenin mRNA abundance. Conditional deletion of both C/EBPα alleles further diminishes C/EBPα mRNA levels, however, rather than ablating amelogenin expression, we observe wild-type amelogenin mRNA abundance levels. We examined C/EBPβ and NF-YA expression, two transcription factors that had previously been shown to modestly participate in amelogenin expression, in vitro, but found no significant changes in either of their mRNA abundance levels comparing conditional knock-out mice with wild-type counterparts. While the abundance of C/EBPδ is also unchanged in C/EBPα conditional knock-out mice, in vitro, we find that C/EBPδ activates the mouse amelogenin promoter and synergistically cooperates with NF-Y, suggesting that C/EBPδ can functionally substitute for C/EBPα to produce an enamel matrix competent to direct biomineralization.
doi:10.1074/jbc.M702097200
PMCID: PMC4445686  PMID: 17704518
16.  The dynamic nature and territory of transcriptional machinery in the bacterial chromosome 
Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP) in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment and highlights the challenges in the study. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid) structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.
doi:10.3389/fmicb.2015.00497
PMCID: PMC4440401  PMID: 26052320
RNA polymerase; bacterial nucleolus; replisome; chromosome territories; growth rate regulation; stress responses; superresolution imaging; E. coli
17.  Intrauterine Growth Restriction Caused by Underlying Congenital Cytomegalovirus Infection 
The Journal of Infectious Diseases  2014;209(10):1573-1584.
Background. Human cytomegalovirus (HCMV) is the major viral etiology of congenital infection and birth defects. Fetal transmission is high (30%–40%) in primary maternal infection, and symptomatic babies have permanent neurological, hearing, and vision defects. Recurrent infection is infrequently transmitted (2%) and largely asymptomatic. Congenital infection is also associated with intrauterine growth restriction (IUGR).
Methods. To investigate possible underlying HCMV infection in cases of idiopathic IUGR, we studied maternal and cord sera and placentas from 19 pregnancies. Anti-HCMV antibodies, hypoxia-related factors, and cmvIL-10 were measured in sera. Placental biopsy specimens were examined for viral DNA, expression of infected cell proteins, and pathology.
Results. Among 7 IUGR cases, we identified 2 primary and 3 recurrent HCMV infections. Virus replicated in glandular epithelium and lymphatic endothelium in the decidua, cytotrophoblasts, and smooth muscle cells in blood vessels of floating villi and the chorion. Large fibrinoids with avascular villi, edema, and inflammation were significantly increased. Detection of viral proteins in the amniotic epithelium indicated transmission in 2 cases of IUGR with primary infection and 3 asymptomatic recurrent infections.
Conclusions. Congenital HCMV infection impairs placental development and functions and should be considered as an underlying cause of IUGR, regardless of virus transmission to the fetus.
doi:10.1093/infdis/jiu019
PMCID: PMC3997585  PMID: 24403553
congenital; HCMV; IUGR; pregnancy; fetus; placenta; villi; chorion; amnion; blood vessels
18.  Significance of platelet count and platelet-based models for hepatocellular carcinoma recurrence 
AIM: To explore the effects of platelet count (PLT) and 11 platelet-based indices on postoperative recurrence of hepatocellular carcinoma (HCC).
METHODS: We retrospectively analyzed 172 HCC patients who were treated by partial hepatectomy. Preoperative data, including laboratory biochemical results, were used to calculate the 11 indices included in the analysis. We performed receiver operating characteristic curve analysis to determine the optimal cut-off values for predicting recurrence. Cumulative rates of HCC recurrence were calculated using Kaplan-Meier survival curves and differences were analyzed by log-rank tests. Multivariate analyses were performed to identify independent predictors of recurrence, early recurrence (within one year after surgery), and late recurrence in HCC. To obtain better prognostic models, PLT-based indices were analyzed separately after being expressed as binary and continuous variables. Two platelet-unrelated, validated HCC prognostic models were included in the analyses as reference indices. Additional analyses were performed after patients were stratified based on hepatitis B virus infection status, cirrhosis, and tumor size to investigate the significance of platelets in different subgroups.
RESULTS: In the study cohort, 44.2% (76/172) of patients experienced HCC recurrence, and 50.6% (87/172) died during a median follow-up time of 46 mo. PLT and five of the 11 platelet-related models were significant predisposing factors for recurrence (P < 0.05). Multivariate analysis indicated that, among the clinical parameters, presence of ascites, PLT ≥ 148 × 109/L, alkaline phosphatase ≥ 116 U/L, and tumor size ≥ 5 cm were independently associated with a higher risk of HCC recurrence (P < 0.05). Independent and significant models included the aspartate aminotransferase/PLT index, fibrosis index based on the four factors, fibro-quotient, aspartate aminotransferase/PLT/γ-glutamyl transpeptidase/alpha-fetoprotein index, and the PLT/age/alkaline phosphatase/alpha-fetoprotein/aspartate aminotransferase index. There were different risk factors between early and late recurrences, and PLT and these indices were more inclined to influence late recurrence. PLT was only predictive of recurrence in non-cirrhotic HCC patients, and was not influenced by tumor size, which was a critical confounder in our study.
CONCLUSION: PLT and PLT-based noninvasive models are effective tools for predicting postoperative recurrence, especially late recurrence. Larger cohorts are needed to validate our findings.
doi:10.3748/wjg.v21.i18.5607
PMCID: PMC4427685  PMID: 25987786
Alkaline phosphatase; Alpha-fetoprotein; Aspartate aminotransferase; Blood platelets; Hepatocellular carcinoma; Recurrence
19.  Signal Regulatory Protein-α Protects Against Cardiac Hypertrophy Via the Disruption of Toll-Like Receptor 4 Signaling 
Hypertension  2013;63(1):96-104.
Signal regulatory protein-α (SIRPA/SIRPα) is a transmembrane protein that is expressed in various tissues, including the heart. Previous studies have demonstrated that SIRPA is involved in multiple biological processes, including macrophage multinucleation, skeletal muscle differentiation, neuronal survival, protection against diabetes mellitus, and negative regulation of immune cells. However, the role of SIRPA in cardiac hypertrophy remains unknown. To examine the role of SIRPA in pathological cardiac hypertrophy, we used SIRPA knockout mice and transgenic mice that overexpressed mouse SIRPA in the heart. Cardiac hypertrophy was evaluated by echocardiographic, hemodynamic, pathological, and molecular analyses. We observed downregulation of SIRPA expression in dilated cardiomyopathy human hearts and in animal hearts after aortic banding surgery. Accordingly, SIRPA−/− mice displayed augmented cardiac hypertrophy, which was accompanied by increased cardiac fibrosis and reduced contractile function, as compared with SIRPA+/+ mice 4 weeks after aortic banding. In contrast, transgenic mice with the cardiac-specific SIRPA overexpression exhibited the opposite phenotype in response to pressure overload. Likewise, SIRPA protected against angiotensin II–induced cardiomyocyte hypertrophy in vitro. Mechanistically, we revealed that SIRPA-mediated protection during cardiac hypertrophy involved inhibition of the Toll-like receptor 4/nuclear factor-κB signaling axis. Furthermore, we demonstrated that the disruption of Toll-like receptor 4 rescued the adverse effects of SIRPA deficiency on pressure overload–triggered cardiac remodeling. Thus, our results identify that SIRPA plays a protective role in cardiac hypertrophy through negative regulation of the Toll-like receptor 4/nuclear factor-κB pathway.
doi:10.1161/HYPERTENSIONAHA.113.01506
PMCID: PMC4422401  PMID: 24101669
cardiomegaly; fibrosis; SIRPA protein; human; TLR4 receptor
20.  Adverse Events of Monoclonal Antibodies Used for Cancer Therapy 
BioMed Research International  2015;2015:428169.
In 1997, the first monoclonal antibody (MoAb), the chimeric anti-CD20 molecule rituximab, was approved by the US Food and Drug administration for use in cancer patients. Since then, the panel of MoAbs that are approved by international regulatory agencies for the treatment of hematopoietic and solid malignancies has continued to expand, currently encompassing a stunning amount of 20 distinct molecules for 11 targets. We provide a brief scientific background on the use of MoAbs in cancer therapy, review all types of monoclonal antibodies-related adverse events (e.g., allergy, immune-related adverse events, cardiovascular adverse events, and pulmonary adverse events), and discuss the mechanism and treatment of adverse events.
doi:10.1155/2015/428169
PMCID: PMC4436450  PMID: 26075239
21.  Genetic polymorphisms of the sortase A gene and social-behavioural factors associated with caries in children: a case–control study 
BMC Oral Health  2015;15:54.
Background
Streptococcus mutans (S. mutans) is the primary etiological agent of dental caries. Sortase is a transpeptidase that anchors several surface proteins to the S. mutans cell wall and has been shown to play a major role in cariogenicity. The purpose of this study was to explore the genetic polymorphisms of the sortase gene (srtA) and the social-behavioural factors associated with dental caries in children with S. mutans.
Methods
In this case–control study, 121 S. mutans strains were separately selected from caries-free children and high-severity caries children for sequencing of the srtA gene. Social and behavioural data were collected by self-administered questionnaires. Genomic DNA was extracted from S. mutans strains and amplified by PCR to obtain the srtA gene. The purified PCR products were sequenced and analysed for mutations with ABI Variant Reporter software. The distribution of missense mutations and the mean of social-behavioural factors were compared between the groups. A multiple logistic regression model was used to control for confounding factors.
Results
The mutation frequencies at loci 168 (P = 0.023) and 470 (P = 0.032) were significantly different between the groups. The best-fitting model showed that greater age, high frequencies of solid sugar consumption, prolonged breastfeeding, a high proportion of visible plaque, and S. mutans with a T at locus 168 of the srtA gene were associated with high-severity caries in children (P < 0.05). Children carrying a G at locus 168 of S. mutans had a decreased risk for high-severity caries (OR = 0.32, 95% CI = 0.12–0.86) compared with those carrying a T.
Conclusions
The present study suggested that the locus 168 missense mutation of the srtA gene may correlate with caries susceptibility in children with S. mutans. In addition, age, duration of breastfeeding, solid sugar consumption, and poor oral hygiene contributed to this complex disease.
doi:10.1186/s12903-015-0039-1
PMCID: PMC4423529  PMID: 25934314
Caries; Gene polymorphisms; srtA; Streptococcus mutans
22.  Optimal Decisions for Organ Exchanges in a Kidney Paired Donation Program 
Statistics in biosciences  2013;6(1):85-104.
The traditional concept of barter exchange in economics has been extended in the modern era to the area of living-donor kidney transplantation, where one incompatible donor-candidate pair is matched to another pair with a complementary incompatibility, such that the donor from one pair gives an organ to a compatible candidate in the other pair and vice versa. Kidney paired donation (KPD) programs provide a unique and important platform for living incompatible donor-candidate pairs to exchange organs in order to achieve mutual benefit. In this paper, we propose novel organ allocation strategies to arrange kidney exchanges under uncertainties with advantages, including (i) allowance for a general utility-based evaluation of potential kidney transplants and an explicit consideration of stochastic features inherent in a KPD program; and (ii) exploitation of possible alternative exchanges when the originally planned allocation cannot be fully executed. This allocation strategy is implemented using an integer programming (IP) formulation, and its implication is assessed via a data-based simulation system by tracking an evolving KPD program over a series of match runs. Extensive simulation studies are provided to illustrate our proposed approach.
doi:10.1007/s12561-013-9082-0
PMCID: PMC4004760  PMID: 24795783
Decision under uncertainty; Expected utility; Integer programming; Probabilistic modeling; Organ exchanges
23.  Combination cytotoxicity of backbone degradable HPMA copolymer gemcitabine and platinum conjugates toward human ovarian carcinoma cells 
Multiblock, backbone degradable HPMA copolymer-drug conjugates containing gemcitabine and DACH platinum (mP-GEM and mP-DACH Pt), respectively were synthesized by reversible addition fragmentation (RAFT) polymerization and subsequent chain extension by click chemistry. Using combination index analysis, the cytotoxicities of the two multiblock conjugates, as single agents and in combination, were evaluated in vitro in A2780 human ovarian cancer cells, with free drugs as controls. The greatest synergistic cytotoxic effect was observed when A2780 cells were sequentially exposed to mP-GEM for 24 h and mP-DACH Pt for 48 h. In addition, mechanistic studies support the rationale of the synergy between mP-GEM and mP-DACH Pt: mP-GEM pretreatment was able to enhance the platinum-DNA adduct accumulation and inhibit cell proliferation to a higher extent than single mPDACH Pt treatment. These observations are useful for the development of combination macromolecular therapeutics for ovarian cancer based on the second-generation backbone degradable HPMA copolymers.
doi:10.1016/j.ejpb.2013.11.008
PMCID: PMC4035385  PMID: 24316339
HPMA copolymers; Biodegradable polymers; Combination therapy; Ovarian cancer; gemcitabine; DACH-Pt
24.  Fructose:Glucose Ratios—A Study of Sugar Self-Administration and Associated Neural and Physiological Responses in the Rat 
Nutrients  2015;7(5):3869-3890.
This study explored whether different ratios of fructose (F) and glucose (G) in sugar can engender significant differences in self-administration and associated neurobiological and physiological responses in male Sprague-Dawley rats. In Experiment 1, animals self-administered pellets containing 55% F + 45% G or 30% F + 70% G, and Fos immunoreactivity was assessed in hypothalamic regions regulating food intake and reward. In Experiment 2, rats self-administered solutions of 55% F + 42% G (high fructose corn syrup (HFCS)), 50% F + 50% G (sucrose) or saccharin, and mRNA of the dopamine 2 (D2R) and mu-opioid (MOR) receptor genes were assessed in striatal regions involved in addictive behaviors. Finally, in Experiment 3, rats self-administered HFCS and sucrose in their home cages, and hepatic fatty acids were quantified. It was found that higher fructose ratios engendered lower self-administration, lower Fos expression in the lateral hypothalamus/arcuate nucleus, reduced D2R and increased MOR mRNA in the dorsal striatum and nucleus accumbens core, respectively, as well as elevated omega-6 polyunsaturated fatty acids in the liver. These data indicate that a higher ratio of fructose may enhance the reinforcing effects of sugar and possibly lead to neurobiological and physiological alterations associated with addictive and metabolic disorders.
doi:10.3390/nu7053869
PMCID: PMC4446784  PMID: 26007337
fructose; glucose; self-administration; hypothalamus; nucleus accumbens; dopamine 2 receptor; mu opioid receptor; fatty acid; hepatic; rat
25.  p21-activated kinase 7 is an oncogene in human osteosarcoma 
Cell Biology International  2014;38(12):1394-1402.
p21-activated kinase 7 (PAK7), also named as PAK5, is a member of Rac/Cdc42-associated Ser/Thr protein kinases. It is overexpressed in some types of cancer such as colorectal and pancreatic cancers. However, the expression status and biological function of PAK7 in osteosarcoma are still ambiguous. To evaluate the expression levels of PAK7 in osteosarcoma tissues and cell lines, immunohistochemistry was used. To investigate the role of PAK7 in cell proliferation, apoptosis and tumorigenicity in vitro and vivo, a recombinant lentivirus expressing PAK7 short hairpin RNA (Lv-shPAK7) was developed and transfected into Saos-2 cells. The silencing effect of PAK7 was confirmed by quantitative real-time PCR (qRT-PCR) and Western blot technique. PAK7 was overexpressed in osteosarcoma tissue and cell line. By knocking-down of PAK7, the proliferation and colony formation of Saos-2 cells were inhibited and apoptosis enhanced significantly. The in vivo tumorigenic ability in xenograft model of Saos-2 cells was also notably inhibited when PAK7 was knocked down. Our results imply that PAK7 promotes cell proliferation and tumorigenesis and may be an attractive candidate for the therapeutic target of osteosarcoma.
doi:10.1002/cbin.10351
PMCID: PMC4410679  PMID: 25052921
cell apoptosis; osteosarcoma; PAK7; tumorigenesis

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